Name: Pelagibaculum spongiae Hp12
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158129

Type strain:

Species: Pelagibaculum spongiae

Strain Designation: Hp12

Culture col. no.: DSM 104963, CECT 9367

Strain history: <- S. Knobloch; Matis ohf., Reykjavik, ICELAND; Hp12<-S. Knobloch; Matís ohf.

NCBI tax ID(s): 2080658 (species)

SI-ID 406450

DSM 104963

Special Collections

Section

Pelagibaculum spongiae Hp12 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from Marine sponge Halichondria panicea.

colony-forming
Gram-negative
motile
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Oceanospirillales*
	Family	*Alcanivoracaceae*
	Genus	*Pelagibaculum*
	Species	**Pelagibaculum spongiae**
	Full Scientific Name (LPSN)	Pelagibaculum spongiae Knobloch et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #67972]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99

[Ref.: #67972]	Cell length	4-38 µm

[Ref.: #67972]	Cell width	1.0-1.2 µm

[Ref.: #67972]	Cell shape	rod-shaped

[Ref.: #67972]	Motility	yes

[Ref.: #67972]	Colony size	1-2 mm
[Ref.: #67972]	Colony color	tan
[Ref.: #67972]	Colony shape	circular
[Ref.: #67972]	Incubation period	3 days
[Ref.: #67972]	Cultivation medium used	Marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #64708]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #64708]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #64708]

Culture medium composition

expand / minimize

[Ref.: #64708]

Culture medium

MARINE AGAR (DSMZ Medium 123)

[Ref.: #64708]

Culture medium growth

[Ref.: #64708]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64708]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #64708]	growth	20 °C
[Ref.: #67972]	growth	4-28 °C
[Ref.: #67972]	optimum	20-22 °C

	Kind of pH		pH
[Ref.: #67972]		optimum	7.0-8.0
[Ref.: #67972]		growth	6.5-9.5
[Ref.: #67972]	no	growth	6
[Ref.: #67972]	no	growth	10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67972]

Oxygen tolerance

aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %91.769

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #67972]		NaCl		growth	1.0-3.0	%(w/v)
[Ref.: #67972]		NaCl		optimum	1.0-2.0	%(w/v)

[Ref.: #67972]	Observation	The major respiratory lipoquinones are Q8 and MK8 with minor amounts of Q7
[Ref.: #67972]	Observation	polar lipid profile contains phosphatidylglycerol and phosphatidylethanolamine as major polar lipids and diphosphatidylglycerol, two uncharacterized aminolipids and three uncharacterized lipids as minor components

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #67972]	adipate ChEBI	-	assimilation
[Ref.: #67972]	casein	-	hydrolysis
[Ref.: #67972]	D-glucose ChEBI	-	assimilation
[Ref.: #67972]	D-glucose ChEBI	-	fermentation
[Ref.: #67972]	D-mannitol ChEBI	-	assimilation
[Ref.: #67972]	D-mannose ChEBI	-	assimilation
[Ref.: #67972]	decanoate ChEBI	-	assimilation
[Ref.: #67972]	esculin ChEBI	+	hydrolysis
[Ref.: #67972]	fumarate ChEBI	-	anaerobic growth
[Ref.: #67972]	gelatin ChEBI	+	hydrolysis
[Ref.: #67972]	L-arabinose ChEBI	-	assimilation
[Ref.: #67972]	malate ChEBI	-	assimilation
[Ref.: #67972]	maltose ChEBI	-	assimilation
[Ref.: #67972]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #67972]	nitrate ChEBI	-	anaerobic growth
[Ref.: #67972]	nitrate ChEBI	+	reduction
[Ref.: #67972]	nitrite ChEBI	-	anaerobic growth
[Ref.: #67972]	phenylacetate ChEBI	-	assimilation
[Ref.: #67972]	potassium gluconate ChEBI	-	assimilation
[Ref.: #67972]	sodium citrate ChEBI	-	assimilation
[Ref.: #67972]	starch ChEBI	-	hydrolysis
[Ref.: #67972]	sulfite ChEBI	-	anaerobic growth
[Ref.: #67972]	thiosulfate ChEBI	-	anaerobic growth
[Ref.: #67972]	tween 20 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #67972]	apramycin ChEBI				yes	10	µg/mL
[Ref.: #67972]	bleomycin ChEBI	yes	10	µg/mL
[Ref.: #67972]	chloramphenicol ChEBI	yes	10	µg/mL
[Ref.: #67972]	kanamycin ChEBI	yes	10	µg/mL
[Ref.: #67972]	nalidixic acid ChEBI	yes	10	µg/mL
[Ref.: #67972]	penicillin ChEBI	yes	10	µg/mL
[Ref.: #67972]	polymyxin b ChEBI	yes	10	µg/mL
[Ref.: #67972]	spectinomycin ChEBI				yes	10	µg/mL
[Ref.: #67972]	spectinomycin ChEBI				yes	30	µg/mL
[Ref.: #67972]	streptomycin ChEBI	yes	10	µg/mL
[Ref.: #67972]	tetracycline ChEBI				yes	10	µg/mL
[Ref.: #67972]	tetracycline ChEBI				yes	30	µg/mL
[Ref.: #67972]	vancomycin ChEBI	yes	10	µg/mL
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Group ID of combined antibiotics	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #67972]		20	ampicillin ChEBI	yes	10	µg/mL
[Ref.: #67972]		20	sulbactam ChEBI	yes	10	µg/mL

	Metabolite production	Metabolite	Production
[Ref.: #67972]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #67972]	acid phosphatase	+	3.1.3.2
[Ref.: #67972]	alkaline phosphatase	+	3.1.3.1
[Ref.: #67972]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #67972]	alpha-fucosidase	-	3.2.1.51
[Ref.: #67972]	alpha-galactosidase	-	3.2.1.22
[Ref.: #67972]	alpha-glucosidase	-	3.2.1.20
[Ref.: #67972]	alpha-mannosidase	-	3.2.1.24
[Ref.: #67972]	arginine dihydrolase	-	3.5.3.6
[Ref.: #67972]	beta-galactosidase	-	3.2.1.23
[Ref.: #67972]	beta-glucosidase	-	3.2.1.21
[Ref.: #67972]	beta-glucuronidase	-	3.2.1.31
[Ref.: #67972]	catalase	-	1.11.1.6
[Ref.: #67972]	cystine arylamidase	-	3.4.11.3
[Ref.: #67972]	cytochrome oxidase	+	1.9.3.1
[Ref.: #67972]	esterase	+
[Ref.: #67972]	esterase Lipase (C 8)	+
[Ref.: #67972]	leucine arylamidase	+	3.4.11.1
[Ref.: #67972]	lipase	-
[Ref.: #67972]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #67972]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #67972]	trypsin	-	3.4.21.4
[Ref.: #67972]	urease	-	3.5.1.5
[Ref.: #67972]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #64708]	Sample type/isolated from	Marine sponge Halichondria panicea
[Ref.: #64708]	Geographic location (country and/or sea, region)	Seltjarnarnes, Grótta lighthouse
[Ref.: #64708]	Country	Iceland
[Ref.: #64708]	Country ISO 3 Code	ISL
[Ref.: #64708]	Continent	Europe

[Ref.: #67972]	Sample type/isolated from	marine sponge H. panicea from the intertidal area
[Ref.: #67972]	Geographic location (country and/or sea, region)	Seltjarnarnes
[Ref.: #67972]	Country	Iceland
[Ref.: #67972]	Country ISO 3 Code	ISL
[Ref.: #67972]	Continent	Europe
[Ref.: #67972]	Geographic location	64.2667°/-22.0000°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Porifera (Sponges)

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67972]	Pelagibaculum spongiae strain Hp12 16S ribosomal RNA gene, partial sequence	MG877746	1530	GenBank ENA	2080658 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67972]	Pelagibaculum spongiae Hp12	GCA_003097315	contig	GenBank ENA	2080658 tax ID

[Ref.: #67972]

GC-content

43 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pelagibaculum spongiae Hp12 NCBI: GCA_003097315.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	84.595	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	64.253	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.769	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.432	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	84.21	no

Availability in culture collections External links

[Ref.: #64708]

Culture collection no.

DSM 104963, CECT 9367

[Ref.: #110965]

SI-ID 406450

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pelagibaculum spongiae gen. nov., sp. nov., isolated from a marine sponge in South-West Iceland.	Knobloch S, Daussin A, Johannsson R, Marteinsson V	Int J Syst Evol Microbiol	10.1099/ijsem.0.003448	2019	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#64708

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104963

#67972

Stephen Knobloch, Aurélien Daussin, Ragnar Jóhannsson, Viggó Marteinsson: Pelagibaculum spongiae gen. nov., sp. nov., isolated from a marine sponge in South-West Iceland. IJSEM 69: 2129 - 2134 2019 ( DOI 10.1099/ijsem.0.003448 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#110965

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID406450.1 )

* These data were automatically processed and therefore are not curated

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